Research workbench
Sfx structure of dye-type peroxidase dtpb in the ferric state
Analyse Sfx structure of dye-type peroxidase dtpb in the ferric state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YRJ
- Type
- protein
- Length
- 1,833 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative iron-dependent peroxidase
- UniProt
- A0A1H2DDB9
- Ligands
- HEM, MG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 26% strand | A0A1H2DDB9 |
| D | Putative iron-dependent peroxidase | protein | 304 | 31% helix, 26% strand | A0A1H2DDB9 |
| E | Putative iron-dependent peroxidase | protein | 305 | 31% helix, 26% strand | A0A1H2DDB9 |
| F | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 26% strand | A0A1H2DDB9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.84 | 0.87 | 88 | empty |
| 2 | 924 | 0.82 | 0.84 | 94 | HEM |
| 3 | 773 | 0.82 | 0.85 | 84 | HEM |
| 4 | 882 | 0.81 | 0.83 | 94 | HEM |
| 5 | 1035 | 0.81 | 0.82 | 94 | HEM |
Interfaces
12 interfaces between chains.
- A–C · 1284 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1257 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1242 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 573 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6YRJ · SFX structure of dye-type peroxidase DtpB in the ferric state · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1H2DDB9
- Elsewhere: RCSB PDB 6YRJ · PDBe 6YRJ · UniProt A0A1H2DDB9
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